If you look at my signature, you'll see I have some of each.
My current EDC lights are 1xCR123A. I don't use 16340s because a) They're lower energy density, b) Eagletac says not to in this light, and c) I don't have any.
I have a few 2xCR123A/1x18650 lights. In those I generally use 18650...